RESEARCH-PGR: Genomic architecture of porous species boundaries: implications for climatic adaptation and hybrid breeding

  • Holliday, Jason J.A. (PI)
  • Keller, Stephen R. (CoPI)
  • Fitzpatrick, Matthew M.C. (CoPI)
  • Hamilton, Jill (CoPI)

Project: Research project

Project Details


Fast-growing poplar trees (Populus spp.) are under intense development for conventional forest products and bioenergy. Poplar hybrids comprise the vast majority of trees in operational plantations due to their superior growth when compared to pure species. However, compared with hybrid crop plants, the undomesticated nature of trees makes predicting performance of their hybrids more challenging. Understanding how variation in hybrid genomes and in the environment lead to desirable (and undesirable) traits has the potential to benefit poplar breeding programs significantly. In this project, natural hybrids between two wide-ranging poplar species - black cottonwood and balsam poplar - are used to characterize, predict, and test how hybridization translates into complex adaptive traits of economic and ecological significance. In addition, a citizen science collaboration with ArbNet, an international community of arboreta, will coordinate establishment of 20 common garden experiments (mini gardens) across North America. These experiments will all be planted with the same set of different poplar genotypes that have had their full genomes sequenced. The project will work with ArbNet to develop a middle school curriculum focused on how traits vary in poplar trees originating from diverse environments. This curriculum will include hands-on collection of data, synthesis of data across sites and illustrating the principles of adaptation and genetic variation. Students will be exposed to biological responses to different environments, experimental design, and hypothesis testing. At each participating university, the project team will also provide interdisciplinary training to the next generation of scientists, spanning field ecology, genomics, and computational biology.

Natural Populus hybrid zones provide a 'living laboratory' in which there has been a long history of natural selection testing the genomic and phenotypic outcomes of hybridization. This project will sample across replicated Populus hybrid zones to capture the history of Genome x Genome x Environment interactions along environmental gradients, and couple this sampling with genome-wide re-sequencing and computational approaches to address the following questions: (i) How is introgression arrayed across the genome and landscape? (ii) What genomic regions control hybrid fitness and what are their environmental drivers? (iii) Can adaptive introgression be recapitulated using controlled crosses? Extensive short and long-read genome resequencing will be combined to characterize genomic variation across the hybrid zones. The team will then use admixture mapping to associate genomic ancestry with climate gradients and adaptive phenotypes, predict hybrid performance across a range of field test sites, and evaluate the contributions of environment and space in explaining patterns of hybridization. Finally, the project will test the repeatability of hybrid outcomes using controlled crosses among Populus species, assessing the predictive value of loci identified as being involved in hybrid vigor/heterosis, and the role of allele-specific expression in generating hybrid phenotypes. This project will provide the most comprehensive picture to date of the genomics of hybridization and heterosis in a tree species and enhance our understanding of the relationship between introgression and fitness across environments.

This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

Effective start/end date6/1/195/31/23


  • National Science Foundation: $2,500,000.00


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